NoncoastalOrdinations-NoMidges
R version 4.0.3 (2020-10-10) – “Bunny-Wunnies Freak Out”
Packages used for NMDS: vegan (version 2.5-7)
Methods
The document shows a series of NMDS ordinations for reference benthic communities in Virginia with environmental characteristics overlaid to evaluate natural differences in community compositions across Virginia. These NMDS will support the Genus level IBI development process. This version excluded chironomidae larvae because they are ubiquitous in all streams in Virginia. No West Virginia DEP data is used in this analysis.Reference sites were evaluated by regional biologists.
The dataset used includes all reference stations collected in Virginia that were deemed reference through a series or water quality parameter filters and regional biologist review. If stations appeared in the dataset more than 4 times, then the most recent 4 samples were used and the rest removed. Samples that had a total number of taxa below 100 collected at the time of sampling were also removed. Taxa that occurred in the dataset <= 5% of the time were removed as well as chironomidae. The data was log10 +1 transformed. Environmental factors were compiled for each station and used to plot over the NMDS to show environmental variation associated with the community matrix. The envfit function in Vegan was used to plot the continuous environmental variables. Some environmental variables like precipitation, slope, and elevation have not been calculated for all watersheds yet and will be added at a later date.
The first step was to read in the reference site bug taxa list and environmental factors dataset for each station. Join the environmental dataset with the bug dataset to account for multiple observations of each station and collection date and time.
Check to make sure the bug and environmental join was successful:
Number of rows in Community Matrix: 684
Number or rows in Environmental Matrix: 686
The data was log10+1 transformed. Rare taxa (<=5%) were removed.
NMDS Results for Non-Coastal Streams, No Midges
## Run 0 stress 0.1750221
## Run 1 stress 0.1753668
## ... Procrustes: rmse 0.006143009 max resid 0.08963673
## Run 2 stress 0.175598
## Run 3 stress 0.1761569
## Run 4 stress 0.1753961
## ... Procrustes: rmse 0.00422188 max resid 0.07193082
## Run 5 stress 0.1756194
## Run 6 stress 0.1754958
## ... Procrustes: rmse 0.00365245 max resid 0.05988129
## Run 7 stress 0.1753981
## ... Procrustes: rmse 0.005070676 max resid 0.09004806
## Run 8 stress 0.1749947
## ... New best solution
## ... Procrustes: rmse 0.003582456 max resid 0.07191637
## Run 9 stress 0.1755872
## Run 10 stress 0.1754962
## Run 11 stress 0.1752516
## ... Procrustes: rmse 0.004368305 max resid 0.07180633
## Run 12 stress 0.1754683
## ... Procrustes: rmse 0.005468474 max resid 0.08884136
## Run 13 stress 0.1758301
## Run 14 stress 0.1761033
## Run 15 stress 0.1754462
## ... Procrustes: rmse 0.004641448 max resid 0.0903285
## Run 16 stress 0.1749315
## ... New best solution
## ... Procrustes: rmse 0.002536253 max resid 0.04357374
## Run 17 stress 0.1755899
## Run 18 stress 0.1764751
## Run 19 stress 0.1761492
## Run 20 stress 0.1754226
## ... Procrustes: rmse 0.003358587 max resid 0.05898032
## Run 21 stress 0.1754622
## Run 22 stress 0.1755913
## Run 23 stress 0.1757294
## Run 24 stress 0.1752852
## ... Procrustes: rmse 0.00438856 max resid 0.05979287
## Run 25 stress 0.1755992
## Run 26 stress 0.1758642
## Run 27 stress 0.1755712
## Run 28 stress 0.1753683
## ... Procrustes: rmse 0.004934544 max resid 0.09011128
## Run 29 stress 0.1761201
## Run 30 stress 0.1756628
## Run 31 stress 0.1755117
## Run 32 stress 0.1750432
## ... Procrustes: rmse 0.003918715 max resid 0.07220125
## Run 33 stress 0.1757856
## Run 34 stress 0.1751526
## ... Procrustes: rmse 0.00369079 max resid 0.05967223
## Run 35 stress 0.1754709
## Run 36 stress 0.175591
## Run 37 stress 0.1763989
## Run 38 stress 0.1760008
## Run 39 stress 0.1758583
## Run 40 stress 0.1751807
## ... Procrustes: rmse 0.002133436 max resid 0.05494892
## Run 41 stress 0.1758494
## Run 42 stress 0.1760807
## Run 43 stress 0.1752599
## ... Procrustes: rmse 0.003682042 max resid 0.07193889
## Run 44 stress 0.1756126
## Run 45 stress 0.1759101
## Run 46 stress 0.175621
## Run 47 stress 0.1752074
## ... Procrustes: rmse 0.003556397 max resid 0.05982625
## Run 48 stress 0.1752168
## ... Procrustes: rmse 0.00312508 max resid 0.05485244
## Run 49 stress 0.1760547
## Run 50 stress 0.1752102
## ... Procrustes: rmse 0.004545455 max resid 0.08945991
## Run 51 stress 0.1758887
## Run 52 stress 0.1752244
## ... Procrustes: rmse 0.004360554 max resid 0.07151587
## Run 53 stress 0.1749314
## ... New best solution
## ... Procrustes: rmse 0.0002700522 max resid 0.00513614
## ... Similar to previous best
## *** Solution reached##
## Call:
## metaMDS(comm = NoncoastalFive[, 6:105], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NoncoastalFive[, 6:105]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1749314
## Stress type 1, weak ties
## Two convergent solutions found after 53 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NoncoastalFive[, 6:105]'
## NMDS1 NMDS2 r2 Pr(>r)
## Year 0.99730 0.07344 0.0341 0.06 .
## JulianDate -0.39754 0.91758 0.6883 0.01 **
## Latitude -0.95528 -0.29571 0.0010 0.90
## Longitude -0.81172 -0.58405 0.0020 0.85
## totalArea_sqMile -0.74393 -0.66825 0.3650 0.01 **
## ELEVMEAN 0.95522 0.29589 0.1946 0.01 **
## SLPMEAN 0.94715 0.32079 0.1297 0.01 **
## wshdRain_mmyr -0.73251 -0.68076 0.3507 0.01 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 99Plot with Stations: Non-Coastal, No Midges
Season: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Spring
## delta 0.6578 0.6606
## n 346 338
##
## Chance corrected within-group agreement A: 0.04895
## Based on observed delta 0.6592 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Ecoregion: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Northern Piedmont Piedmont
## delta 0.6258 0.6376 0.6765 0.6536
## n 154 40 101 137
## Ridge and Valley
## delta 0.6959
## n 252
##
## Chance corrected within-group agreement A: 0.04007
## Based on observed delta 0.6654 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Basin: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Middle James-Upper New Potomac-Lower
## delta 0.5664 0.5829 0.6499 0.6919 0.6936 0.6909
## n 12 4 61 114 78 25
## Potomac-Shenandoah Rappahannock Roanoke Tennessee-Big Sandy
## delta 0.6941 0.6661 0.651 0.6382
## n 41 122 87 16
## Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.6567 0.6576 0.6057 0.6101
## n 50 53 4 17
##
## Chance corrected within-group agreement A: 0.03804
## Based on observed delta 0.6668 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Admin Region: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO VRO
## delta 0.6845 0.685 0.629 0.6676 0.6797
## n 244 158 17 156 109
##
## Chance corrected within-group agreement A: 0.02096
## Based on observed delta 0.6786 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999##Bioregion: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Bioregion, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Mountain Piedmont
## delta 0.6838 0.6742
## n 446 238
##
## Chance corrected within-group agreement A: 0.01823
## Based on observed delta 0.6805 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Sample Method: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.613 0.6919
## n 9 675
##
## Chance corrected within-group agreement A: 0.003297
## Based on observed delta 0.6909 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Stream Order: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5
## delta 0.6654 0.6917 0.6554 0.6047 0.5677
## n 243 205 137 74 25
##
## Chance corrected within-group agreement A: 0.04619
## Based on observed delta 0.6611 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Stream Order Categories: Non-coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$StreamCate, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Large Medium Small
## delta 0.5975 0.6554 0.6858
## n 99 137 448
##
## Chance corrected within-group agreement A: 0.03781
## Based on observed delta 0.6669 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Water Quality Standard Class: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI
## delta 0.679 0.6806 0.6672 0.6346
## n 210 184 87 203
##
## Chance corrected within-group agreement A: 0.04094
## Based on observed delta 0.6648 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Natural Trout Water WQS: Non-Coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$WQS_TROUT, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Yes
## delta 0.4618 0.3393
## n 394 290
##
## Chance corrected within-group agreement A: 0.01637
## Based on observed delta 0.4098 and expected delta 0.4167
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Bioregion and Season, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$BioregionSeason, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MountainFall MountainSpring PiedmontFall PiedmontSpring
## delta 0.6529 0.6453 0.6227 0.6517
## n 225 221 121 117
##
## Chance corrected within-group agreement A: 0.06963
## Based on observed delta 0.6449 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999Bioregion, Stream Size and Season: Non-coastal, No Midges
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:105], grouping = samplescoresenv_noncoast$Bioregionsize, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## LargeMountainFall LargeMountainSpring LargePiedmontFall
## delta 0.4967 0.5818 0.5395
## n 29 27 22
## LargePiedmontSpring MediumMountainFall MediumMountainSpring
## delta 0.5779 0.5996 0.6062
## n 21 51 50
## MediumPiedmontFall MediumPiedmontSpring SmallMountainFall
## delta 0.5868 0.6522 0.6408
## n 18 18 145
## SmallMountainSpring SmallPiedmontFall SmallPiedmontSpring
## delta 0.6138 0.6164 0.6305
## n 144 81 78
##
## Chance corrected within-group agreement A: 0.1189
## Based on observed delta 0.6107 and expected delta 0.6931
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999